Transcriptional landscape of Atractylodes chinensis contracting root rot

Atractylodes chinensis is among the most economically valuable medicinal plants, serving as the primary source of Atractylodis rhizoma. Its pharmacological activities in treating digestive and urinary disorders have been officially recognized in both the Chinese and Japanese Pharmacopoeias. Whereas, the natural scarcity of Atractylodes chinensis necessitates enhanced cultivation strategies, particularly targeting root rot resistance to ameliorate crop yield and sustainable production. This study implemented controlled cultivation of Atractylodes chinensis and collected rhizome samples exhibiting early-stage root rot symptoms, advanced necrosis, and healthy controls. Ultra-high throughput sequencing was employed to detect differentially expressed genes (DEGs). Key dysregulated genes under root rot infection were systematically screened through Reactome pathway enrichment analysis, followed by clarification of cascade signaling. Further findings were validated through chromosomal mapping, correlation analysis, co-expression profiling, and dynamic protein interaction studies. Four critical genes annotated as probable sucrose-phosphate synthase 3, UDP-glucose 6-dehydrogenase 1-like, UDP-D-apiose/UDP-D-xylose synthase 2, and granule-bound starch synthase 1 demonstrated incipient infection expression patterns. Their dysregulation correlated with reduced nodule formation, diminished nitrogenase activity, disrupted cell wall integrity, and elevated reactive oxygen species levels. Twenty-nine progressive DEGs revealed functional connections to critical physiological processes including one-carbon metabolism, transmethylation-feedback regulation, polarity along the adaxial-abaxial axis, and synthesis of amino acid and phytoalexin. Notably, ten DEGs exhibited continuous dysregulation throughout infection progression, coupled with impaired response to metal stresses, potassium loss, and pathogens infection. This investigation systematically delineates the stage-specific pathological gene network underlying Atractylodes chinensis root rot pathogenesis, providing molecular targets for future disease-resistant cultivar development.